Comparative genomic analysis between Lactobacillus delbreuckii subsp. lactis and Lactobacillus delbreuckii subsp. bulgaricus of dairy origin

Lactobacillus delbreuckii subsp. lactis and Lactobacillus delbreuckii subsp. bulgaricus are lactic acid bacteria commonly exploited by the dairy industry as starter cultures, mainly for the production of cheese and yogurt. In this work, we present the comparative genomic analysis between the recently sequenced genomes of L. lactis ACA-DC 178 and L. bulgaricus ACA DC 87, isolated from Kasseri cheese and yogurt, respectively. The genome of L. lactis ACA-DC 178 is larger than that of L. bulgaricus ACA-DC 87, containing 2,048 and 1,928 protein coding genes, respectively. Full chromosome alignments revealed strain specific differences, although a high degree of synteny between the two strains was also observed. The core genome of the two stains contained about 1,300 genes while the unique genes of the two strains were als oidentified. The two genomes contained several genomic islands, indicating that a number of genes have been acquired through horizontal gene transfer. We also predicted one confirmed CRISPR system in each genome, three potential antimicrobial peptides in total and also prophage sequences integrated into the genomes of the two strains. Overall,our analysis provides useful insights into the technological potential of the ACA-DC 178 and ACA-DC 87 strains

Characterization of the dairy Streptococcus thermophilus ACA-DC 29 strain through comparative genomics

Background: Although the Streptococcus genus includes mainly pathogenic species, Streptococcus thermophilus is a widely used dairy starter culture of great economic importance for the food industry. S. thermophilus has been adapted to milk probably through a degenerative evolution process that has led to the loss of typical streptococcal pathogenic traits. Objectives: The genome sequence of the yogurt isolate S. thermophilus ACA-DC 29 was analyzed for assessing the technological potential of this strain. Comparative genomics analysis was also performed between the genome of ACA-DC 29 and the existing complete genome sequences of S. thermophilus. Methods:The genome sequence of ACA-DC 29 was annotated using online annotation tools. Full chromosome alignments were calculated with Progressive Mauve. The pangenome, the core genome and the unique genes were predicted with the GView Server. The genomic islands, the CRISPRs and the antimicrobial peptides were predicted with IslandViewer, CRISPRcompar and BAGEL3, respectively. Conclusions:The analysis of the S. thermophilus ACA-DC 29 genome sequence revealed the absence of pathogenic features. Genes related to the adaptation to milk were identified. Full chromosome alignments showed a high degree of synteny among the different strains. The pangenome of the ten strains comprised of approximately 2,300 genes. Concerning the ACA-DC 29 strain, approximately 250 unique genes involved in various biological processes were also identified. Further analysis indicated that several of them may have been acquired through horizontal gene transfer. Five potential antimicrobial peptides and two CRISPR systems, which may confer resistance against phages, were also predicted

Adaptation of Streptococcus macedonicus and Streptococcus thermophilus in milk. Common strategies, distinct ways.

Lactic acid bacteria (LAB) are the most important bacteria in food fermentations. Among the genera included in LAB is the Streptococcus genus, containing a number of species that are commensals and opportunistic pathogens. Up to now only one species in the Streptococcus genus, Streptococcus thermophilus, has been traditionally used as a starter in milk and is considered a domesticated organism. However, Streptococcus macedonicus, belonging to the S. bovis/S. equinus complex (SBSEC), can be also found in milk. In this study, S. macedonicus was fully sequenced and a comparative analysis was performed against all other SBSEC members. According to our analysis, S. macedonicus missed several genes encoding enzymes for the degradation of complex plant carbohydrates typically met in the genome of Streptococcus gallolyticus, indicating a reduced ability to survive in the gastrointestinal tract of herbivores. In addition, two pilus operons necessary for the adhesion of S. gallolyticus to the host and the initiation of infection were absent from the S. macedonicus genome. Adaptation of S. macedonicus to the milk environment was supported by the presence of an extra lactose operon. Finally, the plasmid pSMA198 found in S. macedonicus also provided evidence about the habituation of the species to milk. Our findings support adaptation of S. macedonicus to the rich in nutrients milk environment characterized by diminished biosynthetic capabilities and loss of pathogenicity-related genes in parallel to gene gain events through horizontal gene transfer, similarly to S. thermophilus. Comparative analysis between S. macedonicus and S. thermophilus though revealed numerous species-specific differences at the genomic and proteomic level, suggesting that common strategies can be used by truly divergent organisms during their evolutionary histor

Comparative genomic analysis among three dairy Streptococcus macedonicusstrains

Streptococcus macedonicus and Streptococcus infantarius, two species within the Streptococcus bovis/ Streptococcus equinus complex (SBSEC) are frequently found in spontaneously fermented foods especially of dairy origin. These two species have been suggested to be non-pathogenic and to have been adapted to the dairy environment similarly to Streptococcus thermophilus. Analysis of the first complete genomes of S. macedonicus and S. infantarius indicated that they may be indeed adapted to milk but they also have retained a restricted repertoire of virulence traits when compared to well characterized pathogenic streptococci. In this study we performed comparative genomic analysis among S. macedonicus strains, isolated from Italian, French and Greek dairy products. The contigs of the Italian and French partial genomes were aligned using as a reference the Greek S. macedonicus ACA-DC 198 genome, the only S. macedonicus genome that is completely sequenced to date. Based on these assemblies, we constructed two distinct pseudochromosomes for the French and the Italian strains. Despite the artifactual nature of the two chromosomes, pairwise alignments among the three genomes revealed a high degree of synteny. The genetic information was overall conserved, but strain specific regions also existed. Furthermore, the analysis revealed that the French S. macedonicus strain has lost genes involved in the catabolism of complex plant carbohydrates, in the adhesion to the host’s cells and in haemolysis. On the other hand, an extra lactose operon and a proteolytic system characteristic of lactic acid bacteria were identified, indicating their evolutionary adaptation to the milk environment. Analogous observations could also be made for the Italian strain. Even though our findings further support the adaptation of the S. macedonicus species to milk fermentation, the analysis of the additional S. macedonicus genomes, including non-dairy isolates, may be necessary to clarify its pathogenic potentia

Discovering probiotic microorganisms: invitro, invivo, genetic and omics approaches

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms

Comparative genomics among dairy strains of Streptococcus thermophilus

Microorganisms like lactic acid bacteria are employed for the biotransformation of raw materials into fermented foods. Fermented foods have increased nutritional value and shelf life as well as improved organoleptic characteristics compared to the raw materials. Interestingly, there are several genera within lactic acid bacteria that are considered to be important for food fermentations including the Streptococcus genus. However, only Streptococcus thermophilus is used as a starter culture. Streptococcus thermophilus has been adapted to milk and dairy products through a reductive evolution process that has led to the loss of typical streptococcal pathogenictraits. In this work we present the comparative genomic analysis among the recently sequenced genome of S. thermophilus ACA-DC 29 is olated from yogurt and the existing seven complete genome sequences of S. thermophilus. Full chromosome alignments revealed a high degree of synteny among the different strains although strain specific differences could also be observed. The pangenome of the eight strains was comprised of approximately 2,300 genes. Concerning the ACA-DC 29 strain, the majority of genes was distributed in the core and the accessory genomes. We also identified a significant percentage of unique genes, i.e. approximately 250, involved in various biological processes. Further analysis of these unique genes revealed that several of them may have been acquired through horizontal gene transfer. We also predicted five potential antimicrobial peptides and two CRISPR systems, which may confer resistance against phages. Overall, our analysis provides useful insights into the technological potential of the ACA-DC 29 strain

Development and evaluation of a web-based breast cancer cultural competency course for primary healthcare providers

<p>Abstract</p> <p>Background</p> <p>To develop and evaluate a continuing medical education (CME) course aimed at improving healthcare provider knowledge about breast cancer health disparities and the importance of cross-cultural communication in provider-patient interactions about breast cancer screening.</p> <p>Methods</p> <p>An interactive web-based CME course was developed and contained information about breast cancer disparities, the role of culture in healthcare decision making, and demonstrated a model of cross-cultural communication. A single group pre-/post-test design was used to assess knowledge changes. Data on user satisfaction was also collected.</p> <p>Results</p> <p>In all, 132 participants registered for the CME with 103 completing both assessments. Differences between pre-/post-test show a significant increase in knowledge (70% vs. 94%; p < .001). Ninety-five percent of participants agreed that the web based training was an appropriate tool to train healthcare providers about cultural competency and health disparities.</p> <p>Conclusion</p> <p>There was an overall high level of satisfaction among all users. Users felt that learning objectives were met and the web-based format was appropriate and easy to use and suggests that web-based CME formats are an appropriate tool to teach cultural competency skills. However, more information is needed to understand how the CME impacted practice behaviors.</p